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Conserved domains on  [gi|6324791|ref|NP_014860|]
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replication factor C subunit 1 [Saccharomyces cerevisiae S288C]

Protein Classification

HLD_clamp_RFC and RFC1 domain-containing protein( domain architecture ID 13042156)

protein containing domains BRCT, HLD_clamp_RFC, and RFC1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 621-776 5.48e-82

Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.


:

Pssm-ID: 462507  Cd Length: 158  Bit Score: 260.20  E-value: 5.48e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    621 ISLGDIVEKKIRSsEQLWSLLPLHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIG 700
Cdd:pfam08519   1 ISDGDLVDRMIRG-EQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6324791    701 LRLDYLPTFRKRLLDPFLKQGADAISSVIEVMDDYYLTKEDWDSIMEFF---VGPDVTTAIIKKIPATVKSGFTRKYNS 776
Cdd:pfam08519  80 LRLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELStwgVGPYGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 298-762 1.14e-47

replication factor C large subunit; Provisional


The actual alignment was detected with superfamily member PRK04195:

Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 177.04  E-value: 1.14e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   298 WTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNsfkhagkdgsgvfRAAMLYGPPGIGKTTAAHLVAQELGYDILEQ 377
Cdd:PRK04195   4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPK-------------KALLLYGPPGVGKTSLAHALANDYGWEVIEL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   378 NASDVRSKTLLNAGVKNALDNMSVVGYfkhneeaqnlngKHFVIIMDEVDGMSG-GDRGGVGQLAQFCRKTSTPLILICN 456
Cdd:PRK04195  71 NASDQRTADVIERVAGEAATSGSLFGA------------RRKLILLDEVDGIHGnEDRGGARAILELIKKAKQPIILTAN 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   457 ERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENI 536
Cdd:PRK04195 139 DPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDV 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   537 NEISkawEKNIALKPFDIAHKMLDGQIYSDIgsrnftlndKIALYFDDFDFTPLM--IQENYlstrPSVLKPgqshLEAV 614
Cdd:PRK04195 219 KTLG---RRDREESIFDALDAVFKARNADQA---------LEASYDVDEDPDDLIewIDENI----PKEYDD----PEDI 278

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   615 AEAANCISLGDIVEKKIRSSeQLWSLLP--LHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEI--HYHT 690
Cdd:PRK04195 279 ARAYDALSRADIFLGRVKRT-QNYDLWRyaSDLMTAGVALAKEKKKRGFTRYQPPSYWRLLSKTKEKRETRDSIakKIAE 357

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324791   691 RLGTSTDKIglRLDYLPTFRKrlldpFLKQGADaissVIEVMDDYY-LTKEDwdsiMEFFVGPDVTTAIIKKI 762
Cdd:PRK04195 358 KLHTSKRKV--RREVLPFLSI-----IFKHNPE----LAARLAAFLeLTEEE----IEFLTGSKKATKKIKKI 415
BRCT super family cl00038
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 153-230 4.88e-33

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


The actual alignment was detected with superfamily member cd17752:

Pssm-ID: 469589 [Multi-domain]  Cd Length: 79  Bit Score: 121.94  E-value: 4.88e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791  153 GKPNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLI 230
Cdd:cd17752   1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLI 78
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 621-776 5.48e-82

Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.


Pssm-ID: 462507  Cd Length: 158  Bit Score: 260.20  E-value: 5.48e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    621 ISLGDIVEKKIRSsEQLWSLLPLHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIG 700
Cdd:pfam08519   1 ISDGDLVDRMIRG-EQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6324791    701 LRLDYLPTFRKRLLDPFLKQGADAISSVIEVMDDYYLTKEDWDSIMEFF---VGPDVTTAIIKKIPATVKSGFTRKYNS 776
Cdd:pfam08519  80 LRLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELStwgVGPYGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 298-762 1.14e-47

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 177.04  E-value: 1.14e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   298 WTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNsfkhagkdgsgvfRAAMLYGPPGIGKTTAAHLVAQELGYDILEQ 377
Cdd:PRK04195   4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPK-------------KALLLYGPPGVGKTSLAHALANDYGWEVIEL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   378 NASDVRSKTLLNAGVKNALDNMSVVGYfkhneeaqnlngKHFVIIMDEVDGMSG-GDRGGVGQLAQFCRKTSTPLILICN 456
Cdd:PRK04195  71 NASDQRTADVIERVAGEAATSGSLFGA------------RRKLILLDEVDGIHGnEDRGGARAILELIKKAKQPIILTAN 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   457 ERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENI 536
Cdd:PRK04195 139 DPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDV 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   537 NEISkawEKNIALKPFDIAHKMLDGQIYSDIgsrnftlndKIALYFDDFDFTPLM--IQENYlstrPSVLKPgqshLEAV 614
Cdd:PRK04195 219 KTLG---RRDREESIFDALDAVFKARNADQA---------LEASYDVDEDPDDLIewIDENI----PKEYDD----PEDI 278

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   615 AEAANCISLGDIVEKKIRSSeQLWSLLP--LHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEI--HYHT 690
Cdd:PRK04195 279 ARAYDALSRADIFLGRVKRT-QNYDLWRyaSDLMTAGVALAKEKKKRGFTRYQPPSYWRLLSKTKEKRETRDSIakKIAE 357

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324791   691 RLGTSTDKIglRLDYLPTFRKrlldpFLKQGADaissVIEVMDDYY-LTKEDwdsiMEFFVGPDVTTAIIKKI 762
Cdd:PRK04195 358 KLHTSKRKV--RREVLPFLSI-----IFKHNPE----LAARLAAFLeLTEEE----IEFLTGSKKATKKIKKI 415
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 153-230 4.88e-33

BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349383 [Multi-domain]  Cd Length: 79  Bit Score: 121.94  E-value: 4.88e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791  153 GKPNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLI 230
Cdd:cd17752   1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLI 78
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
158-231 5.63e-19

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 92.01  E-value: 5.63e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6324791  158 LLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGpKKLEKIKQLKIKAIDEEGFKQLIA 231
Cdd:COG0272 596 LAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILDEAEFLELLG 668
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 158-232 1.08e-16

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 84.79  E-value: 1.08e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6324791   158 LLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGpKKLEKIKQLKIKAIDEEGFKQLIAG 232
Cdd:PRK07956 591 LAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLDEEEFLRLLGE 664
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 350-465 1.38e-13

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 69.10  E-value: 1.38e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  350 MLYGPPGIGKTTAAHLVAQEL---GYDILEQNASDVRSKTLLNAGVKNaldnmsvvgYFKHNEEAQNLNGKHFVIIMDEV 426
Cdd:cd00009  23 LLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGH---------FLVRLLFELAEKAKPGVLFIDEI 93

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 6324791  427 DGMSGGDRGGV-GQLAQF----CRKTSTPLILICNERNLPKMRP 465
Cdd:cd00009  94 DSLSRGAQNALlRVLETLndlrIDRENVRVIGATNRPLLGDLDR 137
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
348-521 2.86e-12

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 68.08  E-value: 2.86e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  348 AAMLYGPPGIGKTTAAHLVAQELGYD---------------ILEQNASDVRsktLLNAG-------------VKNALDNM 399
Cdd:COG0470  20 ALLLHGPPGIGKTTLALALARDLLCEnpeggkacgqchsrlMAAGNHPDLL---ELNPEeksdqigidqireLGEFLSLT 96

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  400 SVVGYFKhneeaqnlngkhfVIIMDEVDGMSG-GDRGGvgqlaqfcRKT------STPLILICN--ERNLPKMRpfDRvC 470
Cdd:COG0470  97 PLEGGRK-------------VVIIDEADAMNEaAANAL--------LKTleeppkNTPFILIANdpSRLLPTIR--SR-C 152

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 6324791  471 LDIQFRRPDANSIKSRLmtiaIREkfKLDPNVIDRLIQTTRGDIRQVINLL 521
Cdd:COG0470 153 QVIRFRPPSEEEALAWL----REE--GVDEDALEAILRLAGGDPRAAINLL 197
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 350-439 6.91e-12

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 63.38  E-value: 6.91e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    350 MLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLnAGVKNaldnmsVVGYFkhnEEAQNLNGKhfVIIMDEVDGM 429
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVG-ESEKR------LRELF---EAAKKLAPC--VIFIDEIDAL 69

                          90
                  ....*....|
gi 6324791    430 sGGDRGGVGQ 439
Cdd:pfam00004  70 -AGSRGSGGD 78
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 153-230 3.38e-10

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 56.92  E-value: 3.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791    153 GKPNCLLGLTIVFTGvLPTLERGASEALAKRYGARVTKSISSKTSVVVLgdEAGPKKLEKIKQLKIKAIDEEGFKQLI 230
Cdd:pfam00533   1 PKEKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 350-479 1.63e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 1.63e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791     350 MLYGPPGIGKTTAAHLVAQEL---GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNL--NGKHFVIIMD 424
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALarKLKPDVLILD 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324791     425 EVDGMSGGDRGGVGQ-------LAQFCRKTSTPLILICNERNLP-KMRPFDRVCLDIQFRRPD 479
Cdd:smart00382  86 EITSLLDAEQEALLLlleelrlLLLLKSEKNLTVILTTNDEKDLgPALLRRRFDRRIVLLLIL 148
BRCT smart00292
breast cancer carboxy-terminal domain;
155-230 1.72e-09

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 55.07  E-value: 1.72e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791     155 PNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSK-TSVVVLGDEAGPK-KLEKIKQLKIKAIDEEGFKQLI 230
Cdd:smart00292   1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKtTTHVIVGSPEGGKlELLKAIALGIPIVKEEWLLDCL 78
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 269-640 2.60e-06

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 51.11  E-value: 2.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    269 EERSKKLAATRVSGGHLERDNVVREEdkLWTVKYAPTNLQQVCGNKGSVMKLKNWLanwensKKNSFKHAGKdgsgvfRA 348
Cdd:TIGR00602  47 ARKRGFLSLEQDTGLELSSENLDGNE--PWVEKYKPETQHELAVHKKKIEEVETWL------KAQVLENAPK------RI 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    349 AMLYGPPGIGKTTAAHLVAQELGYDILEQ-NASDVRS-----KTLLNAGVK--NALDNMSVVGYF------KHNEEAQNL 414
Cdd:TIGR00602 113 LLITGPSGCGKSTTIKILSKELGIQVQEWsNPTLPDFqkndhKVTLSLESCfsNFQSQIEVFSEFllratnKLQMLGDDL 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    415 NGKHFVIIMDEVDGMSGGDRGGVGQLAQ--FCRKTSTPLILICNE---------RNL-PKMRPFDRVCLD------IQFR 476
Cdd:TIGR00602 193 MTDKKIILVEDLPNQFYRDTRALHEILRwkYVSIGRCPLVFIITEslegdnnqrRLLfPAETIMNKEILEeprvsnISFN 272

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    477 RPDANSIKSRLMTIAIREKFKLDPNVI-------DRLIQTTRGDIRQVINLL---STISTTTKTINHENINEISKAWEKN 546
Cdd:TIGR00602 273 PIAPTIMKKFLNRIVTIEAKKNGEKIKvpkktsvELLCQGCSGDIRSAINSLqfsSSKSGSLPIKKRMSTKSDAHASKSK 352

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    547 IALKPFdiahKMLDGQIYSDIGSRNFTLNDKIALYfddfdftpLMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDI 626
Cdd:TIGR00602 353 IKGKHS----SNNENQEIQALGGKDVSLFLFRALG--------KILYCKRATLNELDSPRLPSHLSELSRDTLMVGPEEV 420

                         410
                  ....*....|....
gi 6324791    627 VEKKIRSSEQLWSL 640
Cdd:TIGR00602 421 VEMSHMPGDKTFNL 434
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 621-776 5.48e-82

Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.


Pssm-ID: 462507  Cd Length: 158  Bit Score: 260.20  E-value: 5.48e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    621 ISLGDIVEKKIRSsEQLWSLLPLHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIG 700
Cdd:pfam08519   1 ISDGDLVDRMIRG-EQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6324791    701 LRLDYLPTFRKRLLDPFLKQGADAISSVIEVMDDYYLTKEDWDSIMEFF---VGPDVTTAIIKKIPATVKSGFTRKYNS 776
Cdd:pfam08519  80 LRLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELStwgVGPYGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 298-762 1.14e-47

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 177.04  E-value: 1.14e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   298 WTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNsfkhagkdgsgvfRAAMLYGPPGIGKTTAAHLVAQELGYDILEQ 377
Cdd:PRK04195   4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPK-------------KALLLYGPPGVGKTSLAHALANDYGWEVIEL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   378 NASDVRSKTLLNAGVKNALDNMSVVGYfkhneeaqnlngKHFVIIMDEVDGMSG-GDRGGVGQLAQFCRKTSTPLILICN 456
Cdd:PRK04195  71 NASDQRTADVIERVAGEAATSGSLFGA------------RRKLILLDEVDGIHGnEDRGGARAILELIKKAKQPIILTAN 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   457 ERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENI 536
Cdd:PRK04195 139 DPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDV 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   537 NEISkawEKNIALKPFDIAHKMLDGQIYSDIgsrnftlndKIALYFDDFDFTPLM--IQENYlstrPSVLKPgqshLEAV 614
Cdd:PRK04195 219 KTLG---RRDREESIFDALDAVFKARNADQA---------LEASYDVDEDPDDLIewIDENI----PKEYDD----PEDI 278

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   615 AEAANCISLGDIVEKKIRSSeQLWSLLP--LHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEI--HYHT 690
Cdd:PRK04195 279 ARAYDALSRADIFLGRVKRT-QNYDLWRyaSDLMTAGVALAKEKKKRGFTRYQPPSYWRLLSKTKEKRETRDSIakKIAE 357

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324791   691 RLGTSTDKIglRLDYLPTFRKrlldpFLKQGADaissVIEVMDDYY-LTKEDwdsiMEFFVGPDVTTAIIKKI 762
Cdd:PRK04195 358 KLHTSKRKV--RREVLPFLSI-----IFKHNPE----LAARLAAFLeLTEEE----IEFLTGSKKATKKIKKI 415
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 153-230 4.88e-33

BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349383 [Multi-domain]  Cd Length: 79  Bit Score: 121.94  E-value: 4.88e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791  153 GKPNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLI 230
Cdd:cd17752   1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLI 78
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
158-231 5.63e-19

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 92.01  E-value: 5.63e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6324791  158 LLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGpKKLEKIKQLKIKAIDEEGFKQLIA 231
Cdd:COG0272 596 LAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILDEAEFLELLG 668
rfc PRK00440
replication factor C small subunit; Reviewed
 293-587 8.52e-18

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 85.31  E-value: 8.52e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   293 EEDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLanwensKKNSFKHAgkdgsgvfraaMLYGPPGIGKTTAAHLVAQEL-G 371
Cdd:PRK00440   2 MMEEIWVEKYRPRTLDEIVGQEEIVERLKSYV------KEKNMPHL-----------LFAGPPGTGKTTAALALARELyG 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   372 YD----ILEQNASD------VRSKtllnagVKNaLDNMSVVGY--FKhneeaqnlngkhfVIIMDEVDGMSGgD-----R 434
Cdd:PRK00440  65 EDwrenFLELNASDergidvIRNK------IKE-FARTAPVGGapFK-------------IIFLDEADNLTS-DaqqalR 123

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   435 GGVGQLAQFCRktstpLILICN--ERNLPkmrPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG 512
Cdd:PRK00440 124 RTMEMYSQNTR-----FILSCNysSKIID---PIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEG 195

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   513 DIRQVINLLSTISTTTKTINHENINEI-SKAWEKNI------ALK-PFDIAHKMLDG--------------QIYSDIGSR 570
Cdd:PRK00440 196 DMRKAINALQAAAATGKEVTEEAVYKItGTARPEEIremielALNgDFTEAREKLRDlmidyglsgediikQIHREVWSL 275

                        330
                 ....*....|....*....
gi 6324791   571 NFTLNDKIAL--YFDDFDF 587
Cdd:PRK00440 276 DIPEELKVELidAIGEADF 294
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 158-229 3.38e-17

BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349379 [Multi-domain]  Cd Length: 76  Bit Score: 76.75  E-value: 3.38e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6324791  158 LLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGPKKLEKI----KQLKIKAIDEEGFKQL 229
Cdd:cd17748   1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKGEelkaKGLGIKIISEEEFLDL 76
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 158-232 1.08e-16

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 84.79  E-value: 1.08e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6324791   158 LLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGpKKLEKIKQLKIKAIDEEGFKQLIAG 232
Cdd:PRK07956 591 LAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLDEEEFLRLLGE 664
PLN03025 PLN03025
replication factor C subunit; Provisional
 298-536 3.42e-16

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 80.54  E-value: 3.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   298 WTVKYAPTNLQQVCGNKGSVMKLKNWLAnwenskknsfkhagkdgSGVFRAAMLYGPPGIGKTTAAHLVAQEL---GYD- 373
Cdd:PLN03025   3 WVEKYRPTKLDDIVGNEDAVSRLQVIAR-----------------DGNMPNLILSGPPGTGKTTSILALAHELlgpNYKe 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   374 -ILEQNASD------VRSKTLLNAGVKNALDNmsvvgyfkhneeaqnlnGKHFVIIMDEVDGMSGGDRggvgqlaQFCRK 446
Cdd:PLN03025  66 aVLELNASDdrgidvVRNKIKMFAQKKVTLPP-----------------GRHKIVILDEADSMTSGAQ-------QALRR 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   447 T------STPLILICNERNlPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINL 520
Cdd:PLN03025 122 TmeiysnTTRFALACNTSS-KIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNN 200

                        250
                 ....*....|....*.
gi 6324791   521 LSTISTTTKTINHENI 536
Cdd:PLN03025 201 LQATHSGFGFVNQENV 216
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 297-521 1.68e-14

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 75.80  E-value: 1.68e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   297 LWTVKYAPTNLQQVCGNKGSVMKLKNWLAnwenskknsfkhagkdgSGVFRAAMLYGPPGIGKTTAAHLVAQELgY---- 372
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVD-----------------SPNLPHLLVQGPPGSGKTAAVRALAREL-Ygdpw 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   373 --DILEQNASDV--RSKTLLNAG-------VKNALDNMSVVGYFKH--NEEA--QNLNGKHFVIIMDEVDGMSGGdrggv 437
Cdd:PRK12402  66 enNFTEFNVADFfdQGKKYLVEDprfahflGTDKRIRSSKIDNFKHvlKEYAsyRPLSADYKTILLDNAEALRED----- 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   438 GQLA------------QFCRKTSTPLILIcnernlPKMRpfDRvCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDR 505
Cdd:PRK12402 141 AQQAlrrimeqysrtcRFIIATRQPSKLI------PPIR--SR-CLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLEL 211

                        250
                 ....*....|....*.
gi 6324791   506 LIQTTRGDIRQVINLL 521
Cdd:PRK12402 212 IAYYAGGDLRKAILTL 227
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 350-465 1.38e-13

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 69.10  E-value: 1.38e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  350 MLYGPPGIGKTTAAHLVAQEL---GYDILEQNASDVRSKTLLNAGVKNaldnmsvvgYFKHNEEAQNLNGKHFVIIMDEV 426
Cdd:cd00009  23 LLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGH---------FLVRLLFELAEKAKPGVLFIDEI 93

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 6324791  427 DGMSGGDRGGV-GQLAQF----CRKTSTPLILICNERNLPKMRP 465
Cdd:cd00009  94 DSLSRGAQNALlRVLETLndlrIDRENVRVIGATNRPLLGDLDR 137
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
348-521 2.86e-12

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 68.08  E-value: 2.86e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  348 AAMLYGPPGIGKTTAAHLVAQELGYD---------------ILEQNASDVRsktLLNAG-------------VKNALDNM 399
Cdd:COG0470  20 ALLLHGPPGIGKTTLALALARDLLCEnpeggkacgqchsrlMAAGNHPDLL---ELNPEeksdqigidqireLGEFLSLT 96

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  400 SVVGYFKhneeaqnlngkhfVIIMDEVDGMSG-GDRGGvgqlaqfcRKT------STPLILICN--ERNLPKMRpfDRvC 470
Cdd:COG0470  97 PLEGGRK-------------VVIIDEADAMNEaAANAL--------LKTleeppkNTPFILIANdpSRLLPTIR--SR-C 152

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 6324791  471 LDIQFRRPDANSIKSRLmtiaIREkfKLDPNVIDRLIQTTRGDIRQVINLL 521
Cdd:COG0470 153 QVIRFRPPSEEEALAWL----REE--GVDEDALEAILRLAGGDPRAAINLL 197
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 478-539 2.95e-12

helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein clamp loader complex that forms a stable ATP-dependent complex with the sliding clamp, PCNA, which binds specifically to primed DNA. RFC subunits belong to the clamp loader clade of the AAA+ superfamily.


Pssm-ID: 350842 [Multi-domain]  Cd Length: 63  Bit Score: 62.16  E-value: 2.95e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6324791  478 PDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINEI 539
Cdd:cd18140   1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGGVITEEDVYEV 62
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 347-519 3.47e-12

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 69.17  E-value: 3.47e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  347 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTllnagvknaldnmsvVGyfkhnEEAQNL--------NGKH 418
Cdd:COG0464 192 RGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKY---------------VG-----ETEKNLrevfdkarGLAP 251

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  419 FVIIMDEVDGMsGGDRGG---------VGQLAQFCRKTSTPLILIC---NERNLPK--MRPFDRVcldIQFRRPDANSIK 484
Cdd:COG0464 252 CVLFIDEADAL-AGKRGEvgdgvgrrvVNTLLTEMEELRSDVVVIAatnRPDLLDPalLRRFDEI---IFFPLPDAEERL 327

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 6324791  485 S--RLMTiairEKFKLDPNV-IDRLIQTTRG----DIRQVIN 519
Cdd:COG0464 328 EifRIHL----RKRPLDEDVdLEELAEATEGlsgaDIRNVVR 365
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 350-439 6.91e-12

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 63.38  E-value: 6.91e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    350 MLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLnAGVKNaldnmsVVGYFkhnEEAQNLNGKhfVIIMDEVDGM 429
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVG-ESEKR------LRELF---EAAKKLAPC--VIFIDEIDAL 69

                          90
                  ....*....|
gi 6324791    430 sGGDRGGVGQ 439
Cdd:pfam00004  70 -AGSRGSGGD 78
44 PHA02544
clamp loader, small subunit; Provisional
 353-521 7.60e-11

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 64.24  E-value: 7.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   353 GPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTllnagVKNALDNMSvvgyfkhneEAQNLNGKHFVIIMDEVDGMSGG 432
Cdd:PHA02544  50 PSPGTGKTTVAKALCNEVGAEVLFVNGSDCRIDF-----VRNRLTRFA---------STVSLTGGGKVIIIDEFDRLGLA 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   433 D-----RGGVGQLAQFCRktstpLILICNERN--LPKMRpfDRvCLDIQFRRP---DANSIKS----RLMTIAIREKFKL 498
Cdd:PHA02544 116 DaqrhlRSFMEAYSKNCS-----FIITANNKNgiIEPLR--SR-CRVIDFGVPtkeEQIEMMKqmivRCKGILEAEGVEV 187

                        170       180
                 ....*....|....*....|...
gi 6324791   499 DPNVIDRLIQTTRGDIRQVINLL 521
Cdd:PHA02544 188 DMKVLAALVKKNFPDFRRTINEL 210
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 153-230 3.38e-10

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 56.92  E-value: 3.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791    153 GKPNCLLGLTIVFTGvLPTLERGASEALAKRYGARVTKSISSKTSVVVLgdEAGPKKLEKIKQLKIKAIDEEGFKQLI 230
Cdd:pfam00533   1 PKEKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
ligA PRK14351
NAD-dependent DNA ligase LigA; Provisional
 139-232 4.81e-10

NAD-dependent DNA ligase LigA; Provisional


Pssm-ID: 184640 [Multi-domain]  Cd Length: 689  Bit Score: 63.24  E-value: 4.81e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   139 DPDEIVSEIGsfpegkpNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKI 218
Cdd:PRK14351 598 DPQPAESEGG-------DALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDV 670

                         90
                 ....*....|....
gi 6324791   219 KAIDEEGFKQLIAG 232
Cdd:PRK14351 671 PTLDEEEFEELLAE 684
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 350-479 1.63e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 1.63e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791     350 MLYGPPGIGKTTAAHLVAQEL---GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNL--NGKHFVIIMD 424
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALarKLKPDVLILD 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324791     425 EVDGMSGGDRGGVGQ-------LAQFCRKTSTPLILICNERNLP-KMRPFDRVCLDIQFRRPD 479
Cdd:smart00382  86 EITSLLDAEQEALLLlleelrlLLLLKSEKNLTVILTTNDEKDLgPALLRRRFDRRIVLLLIL 148
BRCT smart00292
breast cancer carboxy-terminal domain;
155-230 1.72e-09

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 55.07  E-value: 1.72e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791     155 PNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSK-TSVVVLGDEAGPK-KLEKIKQLKIKAIDEEGFKQLI 230
Cdd:smart00292   1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKtTTHVIVGSPEGGKlELLKAIALGIPIVKEEWLLDCL 78
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 351-521 1.30e-08

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 58.17  E-value: 1.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   351 LYGPPGIGKTTAAHLVAQELGYDILEQNASdvrsktllNAGVKnalDNMSVVgyfkhnEEAQNL--NGKHFVIIMDEV-- 426
Cdd:PRK13342  41 LWGPPGTGKTTLARIIAGATDAPFEALSAV--------TSGVK---DLREVI------EEARQRrsAGRRTILFIDEIhr 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   427 --------------DGMsggdrggvgqlaqfcrktstpLILIC----NernlpkmrPFDRV-------CLDIQFRRPDAN 481
Cdd:PRK13342 104 fnkaqqdallphveDGT---------------------ITLIGatteN--------PSFEVnpallsrAQVFELKPLSEE 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 6324791   482 SIKS---RLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLL 521
Cdd:PRK13342 155 DIEQllkRALEDKERGLVELDDEALDALARLANGDARRALNLL 197
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 320-438 7.49e-07

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 49.59  E-value: 7.49e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  320 LKNWLANW-ENSKKNSFKHAGKDGSGvfRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKtLLNAGVKNaLDN 398
Cdd:cd19481   1 LKASLREAvEAPRRGSRLRRYGLGLP--KGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSK-YVGESEKN-LRK 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6324791  399 MsvvgyFKHNEEAQNLngkhfVIIMDEVDGMsGGDRGGVG 438
Cdd:cd19481  77 I-----FERARRLAPC-----ILFIDEIDAI-GRKRDSSG 105
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 351-426 7.66e-07

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 52.37  E-value: 7.66e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324791  351 LYGPPGIGKTTAAHLVAQELGYDILEQNASdvrsktllNAGVKnalDNMSVVgyfkhnEEAQNL--NGKHFVIIMDEV 426
Cdd:COG2256  54 LWGPPGTGKTTLARLIANATDAEFVALSAV--------TSGVK---DIREVI------EEARERraYGRRTILFVDEI 114
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 335-519 8.12e-07

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 51.93  E-value: 8.12e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  335 FKHAGKD-GSGVfraaMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKtllnagvknaldnmsVVGyfkhnEEAQN 413
Cdd:COG1222 104 FRKYGIEpPKGV----LLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSK---------------YIG-----EGARN 159

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  414 LNgKHF---------VIIMDEVDGMsGGDRGGVGQ-------LAQFCRK----TSTPLILICNERNLPKM------RP-- 465
Cdd:COG1222 160 VR-EVFelarekapsIIFIDEIDAI-AARRTDDGTsgevqrtVNQLLAEldgfESRGDVLIIAATNRPDLldpallRPgr 237

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6324791  466 FDRVcldIQFRRPDANSIKsRLMTIAIReKFKLDPNV-IDRLIQTTRG----DIRQVIN 519
Cdd:COG1222 238 FDRV---IEVPLPDEEARE-EILKIHLR-DMPLADDVdLDKLAKLTEGfsgaDLKAIVT 291
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 269-640 2.60e-06

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 51.11  E-value: 2.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    269 EERSKKLAATRVSGGHLERDNVVREEdkLWTVKYAPTNLQQVCGNKGSVMKLKNWLanwensKKNSFKHAGKdgsgvfRA 348
Cdd:TIGR00602  47 ARKRGFLSLEQDTGLELSSENLDGNE--PWVEKYKPETQHELAVHKKKIEEVETWL------KAQVLENAPK------RI 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    349 AMLYGPPGIGKTTAAHLVAQELGYDILEQ-NASDVRS-----KTLLNAGVK--NALDNMSVVGYF------KHNEEAQNL 414
Cdd:TIGR00602 113 LLITGPSGCGKSTTIKILSKELGIQVQEWsNPTLPDFqkndhKVTLSLESCfsNFQSQIEVFSEFllratnKLQMLGDDL 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    415 NGKHFVIIMDEVDGMSGGDRGGVGQLAQ--FCRKTSTPLILICNE---------RNL-PKMRPFDRVCLD------IQFR 476
Cdd:TIGR00602 193 MTDKKIILVEDLPNQFYRDTRALHEILRwkYVSIGRCPLVFIITEslegdnnqrRLLfPAETIMNKEILEeprvsnISFN 272

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    477 RPDANSIKSRLMTIAIREKFKLDPNVI-------DRLIQTTRGDIRQVINLL---STISTTTKTINHENINEISKAWEKN 546
Cdd:TIGR00602 273 PIAPTIMKKFLNRIVTIEAKKNGEKIKvpkktsvELLCQGCSGDIRSAINSLqfsSSKSGSLPIKKRMSTKSDAHASKSK 352

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    547 IALKPFdiahKMLDGQIYSDIGSRNFTLNDKIALYfddfdftpLMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDI 626
Cdd:TIGR00602 353 IKGKHS----SNNENQEIQALGGKDVSLFLFRALG--------KILYCKRATLNELDSPRLPSHLSELSRDTLMVGPEEV 420

                         410
                  ....*....|....
gi 6324791    627 VEKKIRSSEQLWSL 640
Cdd:TIGR00602 421 VEMSHMPGDKTFNL 434
COG2842 COG2842
Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons]; ...
 349-521 5.77e-06

Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons];


Pssm-ID: 442090 [Multi-domain]  Cd Length: 254  Bit Score: 48.79  E-value: 5.77e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  349 AMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNA-----GVKNALDNMSVVgyfkHNEEAQNLNGKHFVIIM 423
Cdd:COG2842  53 GVVYGESGVGKTTAAREYANRNPNVIYVTASPSWTSKELLEElaeelGIPAPPGTIADL----RDRILERLAGTGRLLII 128

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  424 DEVDGMsggDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRV------CldIQFRRPDANSIKsrlMTIAIREKFK 497
Cdd:COG2842 129 DEADHL---KPKALEELRDIHDETGVGVVLIGMERLPAKLKRYEQLysrigfW--VEFKPLSLEDVR---ALAEAWGELT 200

                       170       180
                ....*....|....*....|....
gi 6324791  498 lDPNVIDRLIQTTRGDIRQVINLL 521
Cdd:COG2842 201 -DPDLLELLHRITRGNLRRLDRTL 223
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
349-521 6.85e-06

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 49.46  E-value: 6.85e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  349 AMLYGPPGIGKTTAAHLVAQELGyDILEQNASDVRS--------KTL----------LNAGVKNALDNMSVVGYFKHNEE 410
Cdd:COG1474  54 VLIYGPTGTGKTAVAKYVLEELE-EEAEERGVDVRVvyvncrqaSTRyrvlsrileeLGSGEDIPSTGLSTDELFDRLYE 132

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  411 AQNLNGKHFVIIMDEVDGMsgGDRGGVGQLAQFCR------KTSTPLILICNerNLPKMRPFD-RV-----CLDIQFRRP 478
Cdd:COG1474 133 ALDERDGVLVVVLDEIDYL--VDDEGDDLLYQLLRaneeleGARVGVIGISN--DLEFLENLDpRVksslgEEEIVFPPY 208

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 6324791  479 DANSIKSRLMTiaiREKFKLDPNVID----RLI-----QTTrGDIRQVINLL 521
Cdd:COG1474 209 DADELRDILED---RAELAFYDGVLSdeviPLIaalaaQEH-GDARKAIDLL 256
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 350-374 1.04e-05

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 46.34  E-value: 1.04e-05
                          10        20
                  ....*....|....*....|....*
gi 6324791    350 MLYGPPGIGKTTAAHLVAQELGYDI 374
Cdd:pfam05496  37 LLYGPPGLGKTTLANIIANEMGVNI 61
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 163-232 2.86e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 47.08  E-value: 2.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791   163 IVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGD--------EAGPKKLEKIKQLK-----IKAIDEEGFKQL 229
Cdd:PRK06195 226 VVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTkdiedlnrEEMSNKLKKAIDLKkkgqnIKFLNEEEFLQK 305


                 ...
gi 6324791   230 IAG 232
Cdd:PRK06195 306 CKE 308
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 351-374 3.54e-05

Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair];


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 47.00  E-value: 3.54e-05
                        10        20
                ....*....|....*....|....
gi 6324791  351 LYGPPGIGKTTAAHLVAQELGYDI 374
Cdd:COG2255  59 LYGPPGLGKTTLAHIIANEMGVNI 82
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 335-374 5.12e-05

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 46.14  E-value: 5.12e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 6324791    335 FKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI 374
Cdd:TIGR00635  19 FIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNL 58
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
351-371 8.66e-05

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 45.51  E-value: 8.66e-05
                         10        20
                 ....*....|....*....|.
gi 6324791   351 LYGPPGIGKTTAAHLVAQELG 371
Cdd:PRK00080  56 LYGPPGLGKTTLANIIANEMG 76
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
350-518 1.57e-04

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 44.10  E-value: 1.57e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  350 MLYGPPGIGKTTAAHLVAQELGYDILEqnasdVRSKTLLNagvknaldnmSVVGyfkhnEEAQNLnGKHF--------VI 421
Cdd:COG1223  39 LFYGPPGTGKTMLAEALAGELKLPLLT-----VRLDSLIG----------SYLG-----ETARNL-RKLFdfarrapcVI 97

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  422 IMDEVDGMsGGDRGG----------VGQLAQFCRKTSTPLILICnERNLPKM------RPFDRVcldIQFRRPDANSIKS 485
Cdd:COG1223  98 FFDEFDAI-AKDRGDqndvgevkrvVNALLQELDGLPSGSVVIA-ATNHPELldsalwRRFDEV---IEFPLPDKEERKE 172

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 6324791  486 rlMTIAIREKFKLDPNV-IDRLIQTTRG----DIRQVI 518
Cdd:COG1223 173 --ILELNLKKFPLPFELdLKKLAKKLEGlsgaDIEKVL 208
BRCT_CTDP1 cd17729
BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar ...
 142-221 2.30e-04

BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar proteins; CTDP1 (EC 3.1.3.16), also termed TFIIF-associating CTD phosphatase, or TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1), promotes the activity of RNA polymerase II through processively dephosphorylating 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. It plays a role in the exit from mitosis by dephosphorylating crucial mitotic substrates (USP44, CDC20 and WEE1) that are required for M-phase-promoting factor (MPF)/CDK1 inactivation.


Pssm-ID: 349361 [Multi-domain]  Cd Length: 97  Bit Score: 40.98  E-value: 2.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  142 EIVSEIgsfpegKPNCLLGLTIVFTGVLPT---LERGASEALAKRYGARVTKSISSKTSVVVlgdeAGPKKLEKIKQ-LK 217
Cdd:cd17729   4 DILPEL------RSKVLKGCVIVFSGVIPTgidPERSRLWKLAESLGAKVVTDLSPRTTHLV----AAKLGTEKVKQaLK 73


                ....
gi 6324791  218 IKAI 221
Cdd:cd17729  74 MPGI 77
Rad17 pfam03215
Rad17 P-loop domain;
293-376 4.54e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 42.25  E-value: 4.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791    293 EEDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLanwensKKNSFKHAGKdgsgvfRAAMLYGPPGIGKTTAAHLVAQELGY 372
Cdd:pfam03215   4 DGGEQWYEKYKPNCLEQLAVHKRKIKDVQEWL------DAMFLENAKH------RILLISGPSGCGKSTVIKELSKELGP 71


                  ....
gi 6324791    373 DILE 376
Cdd:pfam03215  72 KYRE 75
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 347-438 4.85e-04

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 41.71  E-value: 4.85e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  347 RAAMLYGPPGIGKTtaahLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNmsVVGYFKHNEEAQNLNGKH---FVIIM 423
Cdd:cd19504  36 KGILLYGPPGTGKT----LMARQIGKMLNAREPKIVNGPEILNKYVGESEAN--IRKLFADAEEEQRRLGANsglHIIIF 109

                        90       100
                ....*....|....*....|
gi 6324791  424 DEVDGM-----SGGDRGGVG 438
Cdd:cd19504 110 DEIDAIckqrgSMAGSTGVH 129
HLD_clamp cd18133
helical lid domain of clamp loader-like AAA+ proteins; Clamp loader complexes are multisubunit ...
 478-521 4.94e-04

helical lid domain of clamp loader-like AAA+ proteins; Clamp loader complexes are multisubunit complexes that play an important role in DNA replication. They open sliding clamps for assembly and close them around DNA, specifically targeting them to sites where DNA synthesis is initiated and orienting them correctly for replication. The subunits belong to the clamp loader clade of AAA+ superfamily.


Pssm-ID: 350838 [Multi-domain]  Cd Length: 65  Bit Score: 38.99  E-value: 4.94e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 6324791  478 PDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLL 521
Cdd:cd18133   1 LDQEQLKRRLAAIAEQEKLKLDDAALQALAYISEGDLRKALNAL 44
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 347-443 1.05e-03

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 40.74  E-value: 1.05e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  347 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAgvKNALDNMsvvgyFkhnEEAQNLngKHFVIIMDEV 426
Cdd:cd19503  35 RGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSIVSKYLGES--EKNLREI-----F---EEARSH--APSIIFIDEI 102

                        90       100
                ....*....|....*....|..
gi 6324791  427 DGMS---GGDRGGVGQ--LAQF 443
Cdd:cd19503 103 DALApkrEEDQREVERrvVAQL 124
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 329-382 1.26e-03

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 40.20  E-value: 1.26e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 6324791  329 NSKKNSfkhagkdgsGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDV 382
Cdd:cd19512  14 NTKKNK---------GLYRNILFYGPPGTGKTLFAKKLALHSGMDYAIMTGGDV 58
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 347-389 1.56e-03

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 40.03  E-value: 1.56e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 6324791  347 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDV-----RSKTLLN 389
Cdd:cd19510  24 RGYLLYGPPGTGKSSFIAALAGELDYDICDLNLSEVvltddRLNHLLN 71
AAA_17 pfam13207
AAA domain;
352-403 2.80e-03

AAA domain;


Pssm-ID: 463810 [Multi-domain]  Cd Length: 136  Bit Score: 38.76  E-value: 2.80e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 6324791    352 YGPPGIGKTTAAHLVAQELGYDILeqNASDVRSKTLLNAGVKNALDNMSVVG 403
Cdd:pfam13207   1 TGVPGSGKTTQLKKLAEKLGFPHI--SAGDLLREEAKERGLVEDRDEMRKLP 50
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 335-384 3.93e-03

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 38.92  E-value: 3.93e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 6324791  335 FKHAGKDGSgvfRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRS 384
Cdd:cd19518  26 FQHLGVEPP---RGVLLHGPPGCGKTMLANAIAGELKVPFLKISATEIVS 72
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 350-437 5.14e-03

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 38.65  E-value: 5.14e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324791  350 MLYGPPGIGKTTAAHLVAQELGYDILEqnasdVRSKTLLNAGVKNALDNMSVVgyFKHNEEAqnlngKHFVIIMDEVDGM 429
Cdd:cd19527  30 LLYGPPGTGKTLLAKAIATECSLNFLS-----VKGPELINMYIGESEANVREV--FQKARDA-----KPCVIFFDELDSL 97

                        90
                ....*....|...
gi 6324791  430 S-----GGDRGGV 437
Cdd:cd19527  98 ApsrgnSGDSGGV 110
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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